Targeting PDGF signaling of cancer-associated fibroblasts blocks feedback activation of HIF-1α and tumor progression of clear cell ovarian cancer

Ovarian clear cell carcinoma (OCCC) is a gynecological cancer with a dismal prognosis; however, the mechanism underlying OCCC chemoresistance is not well understood. To explore the intracellular networks associated with the chemoresistance, we analyze surgical specimens by performing integrative analyses that combine single-cell analyses and spatial transcriptomics. We find that a chemoresistant OCCC subpopulation with elevated HIF activity localizes mainly in areas populated by cancer-associated fibroblasts (CAFs) with a myofibroblastic phenotype, which is corroborated by quantitative immunostaining. CAF-enhanced chemoresistance and HIF-1α induction are recapitulated in co-culture assays, which show that cancer-derived platelet-derived growth factor (PDGF) contributes to the chemoresistance and HIF-1α induction via PDGF receptor signaling in CAFs. Ripretinib is identified as an effective receptor tyrosine kinase inhibitor against CAF survival. In the co-culture system and xenograft tumors, ripretinib prevents CAF survival and suppresses OCCC proliferation in the presence of carboplatin, indicating that combination of conventional chemotherapy and CAF-targeted agents is effective against OCCC.

Extraction of local structure differences in silica based on unsupervised learning

Silica exhibits a rich phase diagram with numerous stable structures existing at different temperature and pressure conditions, including its glassy form. In large-scale atomistic simulations, due to the small energy difference, several phases may coexist. While, in terms of long-range order, there are clear differences between these phases, their short- or medium-range structural properties are similar for many phases, thus making it difficult to detect the structural differences. In this study, a methodology based on unsupervised learning is proposed to detect the differences in local structures between eight phases of silica, using atomic models prepared by molecular dynamics (MD) simulations. A combination of two-step locality preserving projections (TS-LPP) and locally averaged atomic fingerprints (LAAF) descriptor was employed to find a low-dimensional space in which the differences among all the phases can be detected. From the distance between each structure in the found low-dimensional space, the similarity between the structures can be discussed and subtle local changes in the structures can be detected. Using the obtained low-dimensional space, the β-α transition in quartz at a low temperature was analyzed, as well as the structural evolution during the melt-quench process starting from α-quartz. The proper differentiation and ease of visualization make the present methodology promising for improving the analysis of the structure and properties of glasses, where subtle differences in structure appear due to differences in the temperature and pressure conditions at which they were synthesized.

Lung cancer detection in perioperative patients' exhaled breath with nanomechanical sensor array

INTRODUCTION

Breath analysis using a chemical sensor array combined with machine learning algorithms may be applicable for detecting and screening lung cancer. In this study, we examined whether perioperative breath analysis can predict the presence of lung cancer using a Membrane-type Surface stress Sensor (MSS) array and machine learning.

METHODS

Patients who underwent lung cancer surgery at an academic medical center, Japan, between November 2018 and November 2019 were included. Exhaled breaths were collected just before surgery and about one month after surgery, and analyzed using an MSS array. The array had 12 channels with various receptor materials and provided 12 waveforms from a single exhaled breath sample. Boxplots of the perioperative changes in the expiratory waveforms of each channel were generated and Mann-Whitney U test were performed. An optimal lung cancer prediction model was created and validated using machine learning.

RESULTS

Sixty-six patients were enrolled of whom 57 were included in the analysis. Through the comprehensive analysis of the entire dataset, a prototype model for predicting lung cancer was created from the combination of array five channels. The optimal accuracy, sensitivity, specificity, positive predictive value, and negative predictive value were 0.809, 0.830, 0.807, 0.806, and 0.812, respectively.

CONCLUSION

Breath analysis with MSS and machine learning with careful control of both samples and measurement conditions provided a lung cancer prediction model, demonstrating its capacity for non-invasive screening of lung cancer.

Clonal origin and genomic diversity in Lynch syndrome-associated endometrial cancer with multiple synchronous tumors: Identification of the pathogenicity of MLH1 p.L582H

Lynch syndrome-associated endometrial cancer patients often present multiple synchronous tumors and this assessment can affect treatment strategies. We present a case of a 27-year-old woman with tumors in the uterine corpus, cervix, and ovaries who was diagnosed with endometrial cancer and exhibited cervical invasion and ovarian metastasis. Her family history suggested Lynch syndrome, and genetic testing identified a variant of uncertain significance, MLH1 p.L582H. We conducted immunohistochemical staining, microsatellite instability analysis, and Sanger sequencing for Lynch syndrome-associated cancers in three generations of the family and identified consistent MLH1 loss. Whole-exome sequencing for the corpus, cervical, and ovarian tumors of the proband identified a copy-neutral loss of heterozygosity (LOH) occurring at the MLH1 position in all tumors. This indicated that the germline variant and the copy-neutral LOH led to biallelic loss of MLH1 and was the cause of cancer initiation. All tumors shared a portion of somatic mutations with high mutant allele frequencies, suggesting a common clonal origin. There were no mutations shared only between the cervix and ovary samples. The profiles of mutant allele frequencies shared between the corpus and cervix or ovary indicated that two different subclones originating from the corpus independently metastasized to the cervix or ovary. Additionally, all tumors presented unique mutations in endometrial cancer-associated genes such as ARID1A and PIK3CA. In conclusion, we demonstrated clonal origin and genomic diversity in a Lynch syndrome-associated endometrial cancer, suggesting the importance of evaluating multiple sites in Lynch syndrome patients with synchronous tumors.

Rapidly growing intramuscular lipoma: a unique entity of benign lipomas in children

This report presents a case of an intramuscular lipoma observed in the left back of a healthy female toddler. It was resected after 3 months of observation because of rapid enlargement, raising suspicion of malignancy. Histopathological examination confirmed a diagnosis of intramuscular lipoma without malignant and blastemal components. Intramuscular lipomas are benign neoplasms that mostly appear as a rapidly growing tumour. Several hypotheses regarding the pathogenesis of this characteristic growth pattern have been proposed, including atrophy of the surrounding muscle, reactive adipocytic neoformation and multiple contractive interactions between the lipoma and the surrounding muscle.

Trends in endometrial carcinoma: experience of a single institute for four decades

OBJECTIVE

To determine the current prognosis of endometrial carcinoma in Japan by analyzing long-term trends in endometrial carcinoma at our hospital.

METHODS

We divided 1463 patients with endometrial carcinoma who visited our hospital between 1984 and 2022 into group 1984-1991, group 1992-1999, group 2000-2006, group 2007-2014 and group 2015-2022. Trends were determined using the Jonckheere-Terpstra and Cochran-Armitage tests. Data were analyzed using Cox regression analysis.

RESULTS

When group 2015-2022 was used as a reference in the univariate analysis, the hazard ratios for the other groups were <1. In particular, the hazard ratio for group 2007-2014 was 0.65 (95% confidence interval, 0.47-0.90, P = 0.009), suggesting that the prognosis of group 2015-2022 was worse than that of group 2007-2014 and seemed to be the worst among all prognoses. In multivariate analysis, the hazard ratios for each group were 1.38, 1.42, 1.88, 1.16 and 1, respectively; the group with the worst prognosis changed from group 2015-2022 to group 2000-2006 (hazard ratio, 1.88; 95% confidence interval, 1.27-2.78, P = 0.001). Age and the rate of non-endometrioid carcinoma exhibited significantly increasing trends (P < 0.001 and P < 0.001, respectively), as did the rates of serous and mixed carcinomas (P = 0.001 and 0.024, respectively). The rates of non-endometrioid carcinoma, serous carcinoma and mixed carcinoma were 19.0%, 5.5% and 3.1% in group 2007-2014 and 28.2%, 10.8% and 4.6% in group 2015-2022, respectively.

CONCLUSIONS

The increasing rates of non-endometrioid carcinoma-especially serous and mixed carcinoma-may be associated with the worsening prognosis of endometrial carcinoma at our institution. Careful monitoring is needed to confirm whether this phenomenon is observed throughout Japan.

Refractory ovarian squamous cell carcinoma arising from a seromucinous borderline tumor with squamous overgrowth: A case report

Ovarian squamous cell carcinoma (SCC) is rare, and most cases arise from ovarian teratomas. Herein, we present a case of ovarian SCC arising from an ovarian seromucinous borderline tumor (SMBT) with squamous overgrowth. A 71-year-old woman an underwent emergency laparotomy due to the rupture of a right ovarian tumor suspected to be a borderline or malignant tumor. We performed a total abdominal hysterectomy, bilateral salpingo-oophorectomy, and partial omentectomy. The postoperative diagnosis was stage IC3 ovarian SCC arising from the SMBT with a squamous overgrowth. Subsequently, she underwent six cycles of combination therapy comprising paclitaxel and carboplatin. Two months after the last chemotherapy treatment, she presented with back pain. A CT scan showed a 14 mm pelvic tumor affecting the ureter, leading to right hydronephrosis. The patient underwent tumor resection and ureteroureterostomy. The pathological diagnosis was keratinizing SCC, representing ovarian cancer recurrence. Eight months after the removal of the recurrent tumor, we found a 35 mm recurrent pelvic tumor causing right hydronephrosis. Additionally, a 20 mm pleural dissemination was identified. Comprehensive genome profiling of recurrent tumor revealed genomic abnormalities in TP53, ARID1A, PTEN, PIK3R1, and CDKN2A/2B. Regarding immunotherapy biomarkers, the microsatellite instability test result was negative, the tumor mutation burden was low, and PD-L1 was highly expressed. The patient was referred to another hospital for participation in an immunotherapy clinical trial for ovarian SCC. This case indicates that refractory ovarian SCC can arise from SMBT. Further evaluation of additional cases is required to identify the molecular biological characteristics of ovarian SCC.

SLFN11 is a BRCA Independent Biomarker for the Response to Platinum-Based Chemotherapy in High-Grade Serous Ovarian Cancer and Clear Cell Ovarian Carcinoma

BRCA1/2 mutations are robust biomarkers for platinum-based chemotherapy in epithelial ovarian cancers. However, BRCA1/2 mutations in clear cell ovarian carcinoma (CCC) are less frequent compared with high-grade serous ovarian cancer (HGSC). The discovery of biomarkers that can be applied to CCC is an unmet need in chemotherapy. Schlafen 11 (SLFN11) has attracted attention as a novel sensitizer for DNA-damaging agents including platinum. In this study, we investigated the utility of SLFN11 in HGSC and CCC for platinum-based chemotherapy. SLFN11 expression was analyzed retrospectively by IHC across 326 ovarian cancer samples. The clinicopathologic significance of SLFN11 expression was analyzed across 57 advanced HGSC as a discovery set, 96 advanced HGSC as a validation set, and 57 advanced CCC cases, all of whom received platinum-based chemotherapy. BRCA1/2 mutation was analyzed using targeted-gene sequencing. In the HGSC cohort, the SLFN11-positive and BRCA mutation group showed significantly longer whereas the SLFN11-negative and BRCA wild-type group showed significantly shorter progression-free survival and overall survival. Moreover, SLFN11-positive HGSC shrunk significantly better than SLFN11-negative HGSC after neoadjuvant chemotherapy. Comparable results were obtained with CCC but without consideration of BRCA1/2 mutation due to a small population. Multivariate analysis identified SLFN11 as an independent factor for better survival in HGSC and CCC. The SLFN11-dependent sensitivity to platinum and PARP inhibitors were validated with genetically modified non-HGSC ovarian cancer cell lines. Our study reveals that SLFN11 predicts platinum sensitivity in HGSC and CCC independently of BRCA1/2 mutation status, indicating that SLFN11 assessment can guide treatment selection in HGSC and CCC.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Human-Machine Collaboration for Accelerated Discovery of Promising Oxygen Evolution Electrocatalysts with On-Demand Elements

A drastically efficient method for identifying electrocatalysts with desirable functionality is a pressing necessity for making a breakthrough in advanced water-electrolyzers toward large-scale green hydrogen production and addressing the significant challenge of carbon neutrality. Despite extensive investigations over the last several centuries, it remains a time-consuming task to identify even one promising affordable electrocatalyst without platinum-group-metal (PGM) for one electrochemical reaction due to its great complexities, particularly for the key anode reaction in the water-electrolyzer of the oxygen evolution reaction (OER). In this study, we demonstrate that a human-machine collaboration based on stepwise-evolving artificial intelligence (se-AI) can significantly shorten the development period of PGM-free multimetal OER electrocatalysts with performance beyond a PGM of RuO2. We were able to reach optimized materials only after 2% experimental trials of the entire candidate pool. The best PGM-free electrocatalyst discovered exhibited excellent activity comparable to RuO2 and, surprisingly, also demonstrated superior stability with a high current density of up to 1000 mA/cm2 at even pH 9.2, which condition is a thermodynamically challenging for typical PGM-free materials. This work illustrates that human's material discovery can be significantly accelerated through collaboration with AI.

External Esophageal Stenting Technique in Palliation for Tracheal Agenesis in a Case of Esophageal Lung: A Lesson Learned from the Experience for Tracheomalacia

Tracheal agenesis (TA) is a rare congenital anomaly with an incidence of 1 per 50,000 newborns. It appears at birth with severe respiratory distress, cyanosis, and inaudible crying. Prompt esophageal intubation and long-term management of the esophageal airway are essential to overcome this catastrophic condition. In the long-term management, external stenting of the esophageal airway has been reported as promising to support the fragile esophageal wall; this technique was taken from the surgery for tracheomalacia. We experienced a case of an infant with tracheal agenesis whose respiratory status was stabilized after external esophageal stenting. The stenting was performed based on a lesson learned in the extensive experience in the surgical treatment for tracheomalacia, and the surgical techniques for successful stenting are herein described.

Revealing factors influencing polymer degradation with rank-based machine learning

The efficient treatment of polymer waste is a major challenge for marine sustainability. It is useful to reveal the factors that dominate the degradability of polymer materials for developing polymer materials in the future. The small number of available datasets on degradability and the diversity of their experimental means and conditions hinder large-scale analysis. In this study, we have developed a platform for evaluating the degradability of polymers that is suitable for such data, using a rank-based machine learning technique based on RankSVM. We then made a ranking model to evaluate the degradability of polymers, integrating three datasets on the degradability of polymers that are measured by different means and conditions. Analysis of this ranking model with a decision tree revealed factors that dominate the degradability of polymers.

A retrospective study of Pipelle endometrial biopsy for ovarian, fallopian tube, and peritoneal cancers

OBJECTIVES

Although the Pipelle endometrial biopsy is widely performed as a practical and minimally invasive test for endometrial disease(s), its effectiveness in ovarian cancer has not been explored. The aim of the present study was to evaluate the results of Pipelle endometrial biopsy for ovarian, fallopian tube, and peritoneal cancers.

METHODS

A pre-treatment Pipelle-endometrial biopsy was performed in 90 patients with ovarian, fallopian tube, or peritoneal cancers between January 2014 and November 2021. We retrospectively analysed the association between the results of Pipelle endometrial biopsy and clinicopathological data. Moreover, we evaluated their impact on the following treatment in advanced cases initially treated with chemotherapy.

RESULTS

The sensitivity and false-negative rates for Pipelle endometrial biopsy were 25/90 (27.8%) and 65/90 (72.2%) in all patients, respectively, and 23/56 (41.0%) and 33/56 (58.9%) in cases with advanced disease (stages III and IV), respectively. Pipelle-positive endometrial biopsy-positive (Pipelle-positive) was not observed in 29 patients with clinical stage I disease, and Pipelle-positive patients exhibited significantly more high-grade serous carcinomas, and positive peritoneal, endometrial, and cervical cytologies than Pipelle-endometrial biopsy-negative cases. Surgical pathology was confirmed in 23 Pipelle-positive patients, and 17/23 (74.0%) had the same diagnosis as that for Pipelle endometrial biopsy. Conversely, 6/23 (26.0%) patients exhibited a minor diagnostic discrepancy between Pipelle endometrial biopsy and surgical pathology. Nineteen of the 38 (50.0%) patients initially treated with chemotherapy were identified as Pipelle-positive, contributing to a prompt histological diagnosis and pre-treatment tumour sampling. Companion diagnostic tests were performed using Pipelle endometrial biopsy samples from 4 inoperable patients.

CONCLUSION

Although the positive rate of Pipelle endometrial biopsy in ovarian, fallopian tube, and peritoneal cancers is low, Pipelle endometrial biopsy may enable prompt histological diagnosis and initiation of chemotherapy while collecting tumour tissue for genetic testing in some cases with advanced disease.

The Junction Between the Peristaltic and Non-peristaltic Bowel (Shore Break) is Found in the Transition Zone in Hirschsprung's Disease

BACKGROUND

The junction between the peristaltic and non-peristaltic bowel, which is named the "shore break" (SB), observed on endoscopy is thought to be the boundary between normal and abnormal motility in Hirschsprung's disease (HD). The transition zone (TZ), which is the histopathological border, does not have normal motility and should be resected. This study aimed to evaluate the histopathological findings of the SB and determine the association between the SB and TZ.

METHODS

A retrospective review of surgical specimens of patients with HD who underwent preoperative SB marking was conducted. The TZ was defined if nerve hypertrophy, myenteric hypoganglionosis, or partial circumferential aganglionosis was detected.

RESULTS

Ten patients (9 boys and 1 girl) were studied. The median age at surgery was 30 days. The median distance from the anal verge to the marked SB site was 14 cm. No patients manifested any obstructive symptoms resulting from a residual TZ bowel. In eight patients, nerve hypertrophy was identified at the proximal margin and at the SB. Myenteric hypoganglionosis was identified in three patients at the proximal margin and SB. Partial circumferential aganglionosis was identified at the SB in two patients. As a result, in all patients, the pull-through site and SB site had histopathological features indicating TZ.

CONCLUSIONS

The SB is located in the TZ. Our results suggest that the proximal part of the TZ has normal motility and that functional border points may be present in the TZ.

LEVEL OF EVIDENCE

IV.

Mapping stress inside living cells by atomic force microscopy in response to environmental stimuli

The response of cells to environmental stimuli, under either physiological or pathological conditions, plays a key role in determining cell fate toward either adaptive survival or controlled death. The efficiency of such a feedback mechanism is closely related to the most challenging human diseases, including cancer. Since cellular responses are implemented through physical forces exerted on intracellular components, more detailed knowledge of force distribution through modern imaging techniques is needed to ensure a mechanistic understanding of these forces. In this work, we mapped these intracellular forces at a whole-cell scale and with submicron resolution to correlate intracellular force distribution to the cytoskeletal structures. Furthermore, we visualized dynamic mechanical responses of the cells adapting to environmental modulations in situ. Such task was achieved by using an informatics-assisted atomic force microscope (AFM) indentation technique where a key step was Markov-chain Monte Carlo optimization to search for both the models used to fit indentation force-displacement curves and probe geometry descriptors. We demonstrated force dynamics within cytoskeleton, as well as nucleoskeleton in living cells which were subjected to mechanical state modulation: myosin motor inhibition, micro-compression stimulation and geometrical confinement manipulation. Our results highlight the alteration in the intracellular prestress to attenuate environmental stimuli; to involve in cellular survival against mechanical signal-initiated death during cancer growth and metastasis; and to initiate cell migration.

Koopmans' Theorem-Compliant Long-Range Corrected (KTLC) Density Functional Mediated by Black-Box Optimization and Data-Driven Prediction for Organic Molecules

Density functional theory (DFT) is a significant computational tool that has substantially influenced chemistry, physics, and materials science. DFT necessitates parametrized approximation for determining an expected value. Hence, to predict the properties of a given molecule using DFT, appropriate parameters of the functional should be set for each molecule. Herein, we optimize the parameters of range-separated functionals (LC-BLYP and CAM-B3LYP) via Bayesian optimization (BO) to satisfy Koopmans' theorem. Our results demonstrate the effectiveness of the BO in optimizing functional parameters. Particularly, Koopmans' theorem-compliant LC-BLYP (KTLC-BLYP) shows results comparable to the experimental UV-absorption values. Furthermore, we prepared an optimized parameter dataset of KTLC-BLYP for over 3000 molecules through BO for satisfying Koopmans' theorem. We have developed a machine learning model on this dataset to predict the parameters of the LC-BLYP functional for a given molecule. The prediction model automatically predicts the appropriate parameters for a given molecule and calculates the corresponding values. The approach in this paper would be useful to develop new functionals and to update the previously developed functionals.

Determination of hyper-parameters in the atomic descriptors for efficient and robust molecular dynamics simulations with machine learning forces

The atomic descriptors used in machine learning to predict forces are often high dimensional. In general, by retrieving a significant amount of structural information from these descriptors, accurate force predictions can be achieved. On the other hand, to acquire higher robustness for transferability without overfitting, sufficient reduction of descriptors should be necessary. In this study, we propose a method to automatically determine hyperparameters in the atomic descriptors, aiming to obtain accurate machine learning forces while using a small number of descriptors. Our method focuses on identifying an appropriate threshold cut-off for the variance value of the descriptor components. To demonstrate the effectiveness of our method, we apply it to crystalline, liquid, and amorphous structures in SiO₂, SiGe, and Si systems. By using both conventional two-body descriptors and our introduced split-type three-body descriptors, we demonstrate that our method can provide machine learning forces that enable efficient and robust molecular dynamics simulations.

Uptake and Outcomes of Neoadjuvant Chemotherapy Among US Patients With Less Common Epithelial Ovarian Carcinomas

Importance

Randomized clinical trials examining the effectiveness of neoadjuvant chemotherapy (NACT) for advanced ovarian cancer predominantly included patients with high-grade serous carcinomas. The use and outcomes of NACT in less common epithelial carcinomas are understudied.

Objective

To investigate the uptake and survival outcomes in treatment with NACT for less common histologic subtypes of epithelial ovarian cancer.

Design, Setting, and Participants

A retrospective cohort study and systematic literature review with meta-analysis was conducted using the National Cancer Database from 2006 to 2017 and the National Cancer Institute's Surveillance, Epidemiology, and End Results Program from 2006 to 2019. Data analysis was performed from July 2022 to April 2023. The evaluation included patients with stage III to IV ovarian cancer with clear cell, mucinous, or low-grade serous histologic subtypes who received multimodal treatment with surgery and chemotherapy.

Exposures

Exposure assignment per the sequence of treatment: primary debulking surgery (PDS) followed by chemotherapy (PDS group) or NACT followed by interval surgery (NACT group).

Main Outcomes and Measures

Temporal trends and characteristics of NACT use were assessed using multivariable analysis, and overall survival (OS) was assessed with the inverse probability of treatment weighting propensity score.

Results

A total of 3880 patients were examined in the National Cancer Database including 1829 women (median age, 56 [IQR, 49-63] years) with clear cell, 1156 women (median age, 53 [IQR, 42-64] years) with low-grade serous, and 895 women (median age, 57 [IQR, 48-66] years) with mucinous carcinomas. NACT use increased in patients with clear cell (from 10.2% to 16.2%, 58.8% relative increase; P < .001 for trend) or low-grade serous (from 7.7% to 14.2%, 84.4% relative increase; P = .007 for trend) carcinoma during the study period. This association remained consistent in multivariable analysis. NACT use also increased, but nonsignificantly, in mucinous carcinomas (from 8.6% to 13.9%, 61.6% relative increase; P = .07 for trend). Across the 3 histologic subtypes, older age and stage IV disease were independently associated with NACT use. In a propensity score-weighted model, the NACT and PDS groups had comparable OS for clear cell (4-year rates, 31.4% vs 37.7%; hazard ratio [HR], 1.12; 95% CI, 0.95-1.33) and mucinous (27.0% vs 26.7%; HR, 0.90; 95% CI, 0.68-1.19) carcinomas. For patients with low-grade serous carcinoma, NACT was associated with decreased OS compared with PDS (4-year rates, 56.4% vs 81.0%; HR, 2.12; 95% CI, 1.55-2.90). Increasing NACT use and histologic subtype-specific survival association were also found in the Surveillance, Epidemiology, and End Results Program cohort (n = 1447). A meta-analysis of 4 studies, including the current study, observed similar OS associations for clear cell (HR, 1.13; 95% CI, 0.96-1.34; 2 studies), mucinous (HR, 0.93; 95% CI, 0.71-1.21; 2 studies), and low-grade serous (HR, 2.11; 95% CI, 1.63-2.74; 3 studies) carcinomas.

Conclusions and Relevance

Despite the lack of data on outcomes of NACT among patients with less common carcinomas, this study noted that NACT use for advanced disease has gradually increased in the US. Primary chemotherapy for advanced-stage, low-grade serous ovarian cancer may be associated with worse survival compared with PDS.

Successful treatment of advanced squamous cell carcinoma arising from mature cystic teratoma of the ovary with homologous recombination deficiency: A case report

INTRODUCTION AND IMPORTANCE

Squamous cell carcinoma (SCC) arising from mature cystic teratoma of the ovary (MCT-SCC) has a poor prognosis at advanced stages. Although the relationship between homologous recombination deficiency (HRD) and platinum-based chemotherapy sensitivity or poly (ADP ribose) polymerase (PARP) inhibitor efficacy in epithelial ovarian cancer has been demonstrated in clinical trials, the significance of HRD status in MCT-SCC has not previously been described.

CASE PRESENTATION

A 73-year-old woman underwent emergency laparotomy due to ovarian tumor rupture. The ovarian tumor was strongly adherent to the surrounding pelvic organs and could not be completely resected. The postoperative diagnosis was stage IIIB MCT-SCC (pT3bNXM0) of the left ovary. After surgery, we conducted the myChoice CDx. The genomic instability (GI) score of 87 was remarkably high, and there was no BRCA1/2 pathogenic mutation. After six courses of combination therapy with paclitaxel and carboplatin, the residual tumors had shrunk by 73 %. We performed interval debulking surgery (IDS), and the residual tumors were completely resected. Subsequently, the patient underwent two courses of the combination of paclitaxel, carboplatin, and bevacizumab, followed by maintenance therapy with olaparib and bevacizumab. Twelve months after IDS, no recurrence has been observed.

CLINICAL DISCUSSION

The present case suggests that there are some HRD cases among MCT-SCC patients and that IDS and maintenance therapy with PARP inhibitors may be effective in such cases, as in epithelial ovarian cancer.

CONCLUSION

Although the frequency of HRD-positive status in MCT-SCC remains unknown, HRD testing may provide appropriate treatment options for advanced MCT-SCC.

Quantum Annealing Designs Nonhemolytic Antimicrobial Peptides in a Discrete Latent Space

Increasing the variety of antimicrobial peptides is crucial in meeting the global challenge of multi-drug-resistant bacterial pathogens. While several deep-learning-based peptide design pipelines are reported, they may not be optimal in data efficiency. High efficiency requires a well-compressed latent space, where optimization is likely to fail due to numerous local minima. We present a multi-objective peptide design pipeline based on a discrete latent space and D-Wave quantum annealer with the aim of solving the local minima problem. To achieve multi-objective optimization, multiple peptide properties are encoded into a score using non-dominated sorting. Our pipeline is applied to design therapeutic peptides that are antimicrobial and non-hemolytic at the same time. From 200 000 peptides designed by our pipeline, four peptides proceeded to wet-lab validation. Three of them showed high anti-microbial activity, and two are non-hemolytic. Our results demonstrate how quantum-based optimizers can be taken advantage of in real-world medical studies.

Falciform ligament hernia: combination of key CT findings

A male patient in his early 90s with no history of abdominal surgery was referred to us for abdominal pain and vomiting. An abdominal computed tomography (CT) demonstrated dilated small bowel with a double beak sign and poorly enhanced wall, which indicated a closed-loop obstruction that leads to strangulation. A closed-loop bowel was located in front of the anterior and medial segments of the liver and to the right of the round ligament of the liver on axial images. Sagittal images revealed that the round ligament has deviated downward and 2 adjacent narrowed intestines were located at its cranial side. These CT findings suggested the hernia orifice was in the falciform ligament. Emergency surgery for highly suspected bowel ischemia revealed the falciform ligament hernia. A combination of the CT findings played a key role, including the double beak sign, the location of the closed-loop small bowel, and the downward deviation of the round ligament, although preoperative CT diagnosis of falciform ligament hernia is a diagnostic challenge.

Population pharmacokinetics and exposure-clinical outcome relationship of remdesivir major metabolite GS-441524 in patients with moderate and severe COVID-19

Although remdesivir, a prodrug of nucleoside analog (GS-441524), has demonstrated clinical benefits in coronavirus disease 2019 (COVID-19) treatment, its pharmacokinetics (PKs) in patients with COVID-19 remain poorly understood. Therefore, in this study, the PKs of remdesivir and its major metabolite, GS-441524, were evaluated using a population PK (PopPK) approach to understand the PK aspect and exposure-clinical outcome relationship. The serum concentrations of remdesivir and GS-441524 (102 points in 39 patients) were measured using liquid chromatography-tandem mass spectrometry. All patients received 200 mg remdesivir on the first day, followed by 100 mg on 2-5 days, except for one patient who discontinued remdesivir on day 4. The median (range) age, body surface area, and estimated glomerular filtration rate (eGFR) were 70 (42-85), 1.74 m² (1.36-2.03), and 68 mL/min/1.73 m² (33-113), respectively. A compartment model with first-order elimination combined with remdesivir and GS-441524 was used for nonlinear mixed-effects model analysis. Remdesivir was rapidly eliminated after infusion, whereas GS-441524 was eliminated relatively slowly (half-time = 17.1 h). The estimated apparent clearance (CL) and distribution volume of GS-441524 were 11.0 L/h (intersubject variability [ISV]% = 43.0%) and 271 L (ISV% = 58.1%), respectively. The CL of GS-441524 was significantly related to the eGFR (CL × [eGFR/68]^0.745 ). The post hoc area under the curve of GS-441524 was unrelated to the recovery rate or aspartate aminotransferase/alanine aminotransferase elevation. Overall, PopPK analysis showed the rapid elimination of remdesivir in the blood, and GS-441524 accumulation depended on eGFR in patients with COVID-19. However, no relevance of exposure-clinical outcome was not suggestive of the dose adjustment of remdesivir.

Spatial genomic diversity associated with APOBEC mutagenesis in squamous cell carcinoma arising from ovarian teratoma

Although the gross and microscopic features of squamous cell carcinoma arising from ovarian mature cystic teratoma (MCT-SCC) vary from case to case, the spatial spreading of genomic alterations within the tumor remains unclear. To clarify the spatial genomic diversity in MCT-SCCs, we performed whole-exome sequencing by collecting 16 samples from histologically different parts of two MCT-SCCs. Both cases showed histological diversity within the tumors (case 1: nonkeratinizing and keratinizing SCC and case 2: nonkeratinizing SCC and anaplastic carcinoma) and had different somatic mutation profiles by histological findings. Mutation signature analysis revealed a significantly enriched apolipoprotein B mRNA editing enzyme catalytic subunit (APOBEC) signature at all sites. Intriguingly, the spread of genomic alterations within the tumor and the clonal evolution patterns from nonmalignant epithelium to cancer sites differed between cases. TP53 mutation and copy number alterations were widespread at all sites, including the nonmalignant epithelium, in case 1. Keratinizing and nonkeratinizing SCCs were differentiated by the occurrence of unique somatic mutations from a common ancestral clone. In contrast, the nonmalignant epithelium showed almost no somatic mutations in case 2. TP53 mutation and the copy number alteration similarities were observed only in nonkeratinizing SCC samples. Nonkeratinizing SCC and anaplastic carcinoma shared almost no somatic mutations, suggesting that each locally and independently arose in the MCT. We demonstrated that two MCT-SCCs with different histologic findings were highly heterogeneous tumors with clearly different clones associated with APOBEC-mediated mutagenesis, suggesting the importance of evaluating intratumor histological and genetic heterogeneity among multiple sites of MCT-SCC.

Comparison of survival rates between incident hemodialysis patients and peritoneal dialysis patients: a 5-year prospective cohort study with propensity score matching

BACKGROUND

The effect of dialytic modality at the start of renal replacement therapy on prognosis is controversial.

METHODS

This multicenter, prospective cohort study included patients undergoing incident hemodialysis (HD) (n = 646) and peritoneal dialysis (PD) (n = 72). We excluded patients who lacked complete data for 3 months. One-to-one propensity score (PS) matching was performed before between-group comparison of survival rates (Kaplan-Meier method and log-rank test) and identification of factors affecting prognosis (Cox proportional-hazards regression analysis).

RESULTS

We enrolled 621 and 71 patients undergoing HD and PD, respectively (overall mean ± standard deviation age: 74 ± 13 years); 20% had cardiovascular disease (CVD). The median follow-up period was 41 (interquartile range 24-66) months. Following PS matching, we analyzed 65 patients undergoing HD and PD each. The 5-year overall survival rates did not differ between the groups (P = 0.97). The PD group exhibited a better CVD-related survival rate (P = 0.03). PD yielded adjusted hazard ratios for all-cause and CVD-related mortality of 0.99 (95% confidence interval [CI] 0.49-1.99, P = 0.97) and 3.92 (95% CI 1.05-14.7, P = 0.04), respectively. Age (P < 0.001) and the use of a central venous catheter (CVC) at dialytic initiation (P = 0.02) were independent risks for all-cause mortality; whereas, only the use of a CVC (P = 0.01) was an independent risk for CVD-related mortality.

CONCLUSION

Although no differences were observed in overall survival, CVD-related survival may be better with dialytic initiation with PD than with HD.

Congenital diaphragmatic hernia survival in an English regional ECMO center

Introduction

Congenital diaphragmatic hernia (CDH) remains a cause of neonatal death. Our aims are to describe contemporary rates of survival and the variables associated with this outcome, contrasting these with our study of two decades earlier and recent reports.

Materials and methods

A retrospective review of all infants diagnosed in a regional center between January 2000 and December 2020 was performed. The outcome of interest was survival. Possible explanatory variables included side of defect, use of complex ventilatory or hemodynamic strategies (inhaled nitric oxide (iNO), high-frequency oscillatory ventilation (HFOV), extracorporeal membrane oxygenation (ECMO), and Prostin), presence of antenatal diagnosis, associated anomalies, birth weight, and gestation. Temporal changes were studied by measuring outcomes in each of four consecutive 63-month periods.

Results

A total of 225 cases were diagnosed. Survival was 60% (134 of 225). Postnatal survival was 68% (134 of 198 liveborn), and postrepair survival was 84% (134 of 159 who survived to repair). Diagnosis was made antenatally in 66% of cases. Variables associated with mortality were the need for complex ventilatory strategies (iNO, HFOV, Prostin, and ECMO), antenatal diagnosis, right-sided defects, use of patch repair, associated anomalies, birth weight, and gestation. Survival has improved from our report of a prior decade and did not vary during the study period. Postnatal survival has improved despite fewer terminations. On multivariate analysis, the need for complex ventilation was the strongest predictor of death (OR=50, 95% CI 13 to 224, p<0.0001), and associated anomalies ceased to be predictive.

Conclusions

Survival has improved from our earlier report, despite reduced numbers of terminations. This may be related to increased use of complex ventilatory strategies.

CRISPR-Cas9-Mediated Knock-In Approach to Insert the GFP11 Tag into the Genome of a Human Cell Line

The protocol in this chapter describes a method to label endogenous proteins using a self-complementing split green fluorescent protein (split GFP_1-10/11) in a human cell line. By directly delivering Cas9/sgRNA ribonucleoprotein (RNP) complexes through nucleofection, this protocol allows for the efficient integration of GFP₁₁ into a specific genomic locus via CRISPR-Cas9-mediated homology-directed repair (HDR). We use the GFP₁₁ sequence in the form of a single-stranded DNA (ssDNA) as an HDR template. Because the ssDNA with less than 200 nucleotides used here is commercially synthesized, this approach remains cloning-free. The integration of GFP11 is performed in cells stably expressing GFP1-10, thereby inducing fluorescence reconstitution. Subsequently, such a reconstituted signal is analyzed using fluorescence flow cytometry for estimating knock-in efficiencies and enriching the GFP-positive cell population. Finally, the enriched cells can be visualized using fluorescence microscopy.

Differences in isolated bacteria between perforated and non-perforated appendicitis: an analysis of 680 consecutive appendicectomies in a single institution

PURPOSE

Escherichia coli and Bacteroides species are the most frequently detected species in ascites in perforated appendicitis and are generally sensitive to non-empiric cephalosporins like cefazolin or cefmetazole. However, monotherapy with such antibiotics is mostly insufficient for perforated appendicitis. To investigate this issue, this study aimed to compare bacterial floras in ascites culture between perforated and non-perforated appendicitis.

METHODS

Ascites culture results in perforated and non-perforated appendicitis cases were analyzed using a departmental database. The duration of symptoms before surgery, pre-surgical white blood cell count, C-reactive protein value, postsurgical length of stay, length of antibiotic treatment, and the rate of using second-line antibiotics or complications were also compared.

RESULTS

A total of 608 and 72 cases of non-perforated and perforated appendicitis were included. Escherichia coli and Bacteroides species were the dominant bacteria in both conditions. However, the total proportions of Pseudomonas aeruginosa, Streptococcus anginosus group, and Enterococcus group were significantly higher in perforated appendicitis than in non-perforated appendicitis.

CONCLUSION

Pseudomonas aeruginosa, Streptococcus anginosus group, and Enterococcus group have better susceptibility to penicillin-based empiric antibiotics than cephalosporins. The abundance of these bacteria might explain why non-empiric cephalosporins are not effective in perforated appendicitis and the superiority of penicillin-based empiric antibiotics.

A case report of atypical anti-glomerular basement membrane disease

Background

Anti-glomerular basement membrane (anti-GBM) disease is characterized by crescentic necrotizing glomerulonephritis, with linear deposits of immunoglobulin G (IgG) in the GBM. Classic anti-GBM disease is clinically associated with rapidly progressive glomerulonephritis with or without pulmonary hemorrhage. Some patients have a better renal prognosis and milder symptoms than those with classic anti-GBM disease, which is termed atypical anti-GBM disease.

Case presentation

A 43-year-old Japanese woman was admitted to our hospital complaining of hematuria that had persisted for more than one month. Serological examination revealed negativity for anti-nuclear, anti-neutrophilic cytoplasmic, and anti-GBM antibodies. However, renal biopsy showed cellular crescents. Immunofluorescence revealed strong diffuse linear capillary loop staining for IgG. An indirect immunofluorescence antibody method was performed by applying the patient serum to normal kidney tissue to confirm the presence of autoantibodies binding to the GBM. Using this method, anti-GBM antibodies were detected. The patient was treated with high-dose steroids, cyclophosphamide, and plasma exchange. Aggressive treatment resolved proteinuria and hematuria and improved renal function.

Conclusions

Renal biopsy is crucial in the diagnosis of anti-GBM disease, especially when serological tests are negative. Accurately identifying the presence of anti-GBM disease is important to initiate optimal treatment.

Visualization of Flow-Induced Strain Using Structural Color in Channel-Free Polydimethylsiloxane Devices

Measuring flow of gases is of fundamental importance yet is typically done with complex equipment. There is, therefore, a longstanding need for a simple and inexpensive means of flow measurement. Here, gas flow is measured using an extremely simple device that consists of an Ar plasma-treated polydimethylsiloxane (PDMS) slab adhered on a glass substrate with a tight seal. This device does not even have a channel, instead, gas can flow between the PDMS and the glass by deforming the PDMS wall, in other words, by making an interstice as a temporary path for the flow. The formation of the temporary path results in a compressive bending stress at the inner wall of the path, which leads to the formation of well-ordered wrinkles, and hence, the emergence of structural color that changes the optical transmittance of the device. Although it is very simple, this setup works sufficiently well to measure arbitrary gases and analyzes their flow rates, densities, and viscosities based on the change in color. It is also demonstrated that this technique is applicable to the flow-induced display of a pattern such as a logo for advanced applications.

QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization

To obtain observable physical or molecular properties such as ionization potential and fluorescent wavelength with quantum chemical (QC) computation, multi-step computation manipulated by a human is required. Hence, automating the multi-step computational process and making it a black box that can be handled by anybody are important for effective database construction and fast realistic material design through the framework of black-box optimization where machine learning algorithms are introduced as a predictor. Here, we propose a Python library, QCforever, to automate the computation of some molecular properties and chemical phenomena induced by molecules. This tool just requires a molecule file for providing its observable properties, automating the computation process of molecular properties (for ionization potential, fluorescence, etc.) and output analysis for providing their multi-values for evaluating a molecule. Incorporating the tool in black-box optimization, we can explore molecules that have properties we desired within the limitation of QC computation.

Involvement of cochlin binding to sulfated heparan sulfate/heparin in the pathophysiology of autosomal dominant late-onset hearing loss (DFNA9)

Late-onset non-syndromic autosomal dominant hearing loss 9 (DFNA9) is a hearing impairment caused by mutations in the coagulation factor C homology gene (COCH). COCH encodes for cochlin, a major component of the cochlear extracellular matrix. Though biochemical and genetic studies have characterized the properties of wild-type and mutated cochlins derived from DFNA9, little is known about the underlying pathogenic mechanism. In this study, we established a cochlin reporter cell, which allowed us to monitor the interaction of cochlin with its ligand(s) by means of a β-galactosidase assay. We found a class of highly sulfated glycosaminoglycans (GAGs), heparin, that were selectively bound to cochlin. The interaction was distinctly abrogated by N-desulfation, but not by 2-O- or 6-O-desulfation. The binding of cochlin to GAG was diminished by all of the point mutations found in DFNA9 patients. Through GAG composition analysis and immunostaining using mouse cochlin/immunoglobulin-Fc fusion protein, we identified moderately sulfated GAGs in mouse cochlea tissue; this implies that cochlin binds to such sulfated GAGs in the cochlea. Since GAGs play an important role in cell growth and survival as co-receptors of signal transduction mechanisms, the interaction of cochlin with GAGs in the extracellular matrix could aid the pathological research of autosomal dominant late-onset hearing loss in DFNA9.

Understanding the evolution of a de novo molecule generator via characteristic functional group monitoring

Recently, artificial intelligence (AI)-enabled de novo molecular generators (DNMGs) have automated molecular design based on data-driven or simulation-based property estimates. In some domains like the game of Go where AI surpassed human intelligence, humans are trying to learn from AI about the best strategy of the game. To understand DNMG's strategy of molecule optimization, we propose an algorithm called characteristic functional group monitoring (CFGM). Given a time series of generated molecules, CFGM monitors statistically enriched functional groups in comparison to the training data. In the task of absorption wavelength maximization of pure organic molecules (consisting of H, C, N, and O), we successfully identified a strategic change from diketone and aniline derivatives to quinone derivatives. In addition, CFGM led us to a hypothesis that 1,2-quinone is an unconventional chromophore, which was verified with chemical synthesis. This study shows the possibility that human experts can learn from DNMGs to expand their ability to discover functional molecules.

Therapeutic Strategies Focused on Cancer-Associated Hypercoagulation for Ovarian Clear Cell Carcinoma

Ovarian clear cell carcinoma (OCCC) is associated with chemotherapy resistance and poor prognosis, especially in advanced cases. Although comprehensive genomic analyses have clarified the significance of genomic alterations such as ARID1A and PIK3CA mutations in OCCC, therapeutic strategies based on genomic alterations have not been confirmed. On the other hand, OCCC is clinically characterized by a high incidence of thromboembolism. Moreover, OCCC specifically shows high expression of tissue factor and interleukin-6, which play a critical role in cancer-associated hypercoagulation and may be induced by OCCC-specific genetic alterations or the endometriosis-related tumor microenvironment. In this review, we focused on the association between cancer-associated hypercoagulation and molecular biology in OCCC. Moreover, we reviewed the effectiveness of candidate drugs targeting hypercoagulation, such as tissue factor- or interleukin-6-targeting drugs, anti-inflammatory drugs, anti-hypoxia signaling drugs, anticoagulants, and combined immunotherapy with these drugs for OCCC. This review is expected to contribute to novel basic research and clinical trials for the prevention, early detection, and treatment of OCCC focused on hypercoagulation.

De novo creation of a naked eye-detectable fluorescent molecule based on quantum chemical computation and machine learning

Designing fluorescent molecules requires considering multiple interrelated molecular properties, as opposed to properties that straightforwardly correlated with molecular structure, such as light absorption of molecules. In this study, we have used a de novo molecule generator (DNMG) coupled with quantum chemical computation (QC) to develop fluorescent molecules, which are garnering significant attention in various disciplines. Using massive parallel computation (1024 cores, 5 days), the DNMG has produced 3643 candidate molecules. We have selected an unreported molecule and seven reported molecules and synthesized them. Photoluminescence spectrum measurements demonstrated that the DNMG can successfully design fluorescent molecules with 75% accuracy (n = 6/8) and create an unreported molecule that emits fluorescence detectable by the naked eye.

Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium

It has become evident that somatic mutations in cancer-associated genes accumulate in the normal endometrium, but spatiotemporal understanding of the evolution and expansion of mutant clones is limited. To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we sequence 1311 endometrial glands from 37 women. By collecting endometrial glands from different parts of the endometrium, we show that multiple glands with the same somatic mutations occupy substantial areas of the endometrium. We demonstrate that “rhizome structures”, in which the basal glands run horizontally along the muscular layer and multiple vertical glands rise from the basal gland, originate from the same ancestral clone. Moreover, mutant clones detected in the vertical glands diversify by acquiring additional mutations. These results suggest that clonal expansions through the rhizome structures are involved in the mechanism by which mutant clones extend their territories. Furthermore, we show clonal expansions and copy neutral loss-of-heterozygosity events occur early in life, suggesting such events can be tolerated many years in the normal endometrium. Our results of the evolutionary dynamics of mutant clones in the human endometrium will lead to a better understanding of the mechanisms of endometrial regeneration during the menstrual cycle and the development of therapies for the prevention and treatment of endometrium-related diseases.

Through regeneration, the endometrium accumulates somatic mutations that can lead to diseases like endometriosis and cancer. Here, the authors use genomics to analyse normal endometrial glands from different patient cohorts, detect rhizome structures with common clonal ancestors and infer clonal expansion dynamics.

Topological alternation from structurally adaptable to mechanically stable crosslinked polymer

Stimuli-responsive polymers with complicated but controllable shape-morphing behaviors are critically desirable in several engineering fields. Among the various shape-morphing materials, cross-linked polymers with exchangeable bonds in dynamic network topology can undergo on-demand geometric change via solid-state plasticity while maintaining the advantageous properties of cross-linked polymers. However, these dynamic polymers are susceptible to creep deformation that results in their dimensional instability, a highly undesirable drawback that limits their service longevity and applications. Inspired by the natural ice strategy, which realizes creep reduction using crystal structure transformation, we evaluate a dynamic cross-linked polymer with tunable creep behavior through topological alternation. This alternation mechanism uses the thermally triggered disulfide-ene reaction to convert the network topology - from dynamic to static - in a polymerized bulk material. Thus, such a dynamic polymer can exhibit topological rearrangement for thermal plasticity at 130°C to resemble typical dynamic cross-linked polymers. Following the topological alternation at 180°C, the formation of a static topology reduces creep deformation by more than 85% in the same polymer. Owing to temperature-dependent selectivity, our cross-linked polymer exhibits a shape-morphing ability while enhancing its creep resistance for dimensional stability and service longevity after sequentially topological alternation. Our design enriches the design of dynamic covalent polymers, which potentially expands their utility in fabricating geometrically sophisticated multifunctional devices.

Integrating Incompatible Assay Data Sets with Deep Preference Learning

A large amount of bioactivity assay data is already accumulated in public databases, but the integration of these data sets for quantitative structure-activity relationship (QSAR) studies is not straightforward due to differences in experimental methods and settings. We present an efficient deep-learning-based approach called Deep Preference Data Integration (DPDI). For integrating outcome variables of different assay types, a surrogate variable is introduced, and a neural network is trained such that the total order induced by the surrogate variable is maximally consistent with given data sets. In a task of predicting efficacy of factor Xa inhibitors, DPDI successfully integrated 2959 molecules distributed in 129 assay data sets. In most of our experiments, data integration improved prediction accuracy strongly in interpolation and extrapolation tasks, indicating that DPDI is an effective tool for QSAR studies.

Surgeon level variation in outcome of repair of congenital diaphragmatic hernia with particular reference to the management of recurrence

INTRODUCTION

The aim of this study is to investigate firstly, the rate of recurrence following primary repair of a congenital diaphragmatic hernia (CDH) and secondly, the rate of recurrence following revisional surgical repair. The primary outcome is rate of recurrence. Secondary outcomes are to establish whether recurrence is related to surgeon, surgeon volume, side of defect, the use of a patch, or a thoracopscopic approach METHODS: All repairs performed in an English regional center over 22 years were recorded. Possible explanatory variables were whether the repair was itself of a recurrence, the surgeon's identity, the surgeon's volume of prior repairs, the side of the defect, the use of a patch.

RESULTS

198 repairs were performed; 170 primary repairs and 28 of recurrences. Failure occurred significantly more commonly among recurrences (32%) than primary repairs (11%), p = 0.005. Failure of the primary repair was significantly more common where a patch was used 8/34 (23%) rather than a sutured repair 10/136 (7%), p = 0.006, or where a thoracoscopic technique was used 4/13 (31%) rather than laparotomy 14/157 (9%) p = 0.01. Failure of the primary repair was unrelated to the identity of the surgeon (Χ² = 5, p = 0.9) or the volume of prior repairs (t = 0.3, p = 0.6). However, failure of repair of a recurrence was significantly related to the surgeon's volume of prior repairs (t = 2.3, p = 0.01) and the identity of the surgeon (Χ² = 17, p = 0.014), but not the use of a patch (Χ² = 1.6, p = 0.2).

CONCLUSIONS

Repair of a recurrence of a CDH has a higher probability of failure than the original repair and is related to both the identity of the surgeon and the prior volume of experience. There is a volume outcome relationship for the repair of recurrence, but not the primary repair of CDH. Our study suggests the repair of recurrence of CDH should be restricted to surgeons with proven outcomes for this procedure.

Vulvar Extramammary Paget Disease Detected by Cytology for Cervical Cancer Screening: A Case Report and Literature Review

Patient: Female, 77-year-old

Final Diagnosis: Secondary extramammary Paget’s disease

Symptoms: Erythema

Medication:—

Clinical Procedure: Biopsy

Specialty: Dermatology • Obstetrics and Gynecology • Oncology • Urology

Novel application of infliximab for diversion colitis

Diversion colitis (DC) that was refractory to standard treatments was successfully treated with infliximab. A 24-year-old man with a transverse colostomy suffered from severe DC. Topical steroids, 5-aminosalicylic acid (5-ASA) enemas and synbiotics were initially effective, and the colostomy was successfully closed with a covering ileostomy to minimise the risk of anastomotic leakage owing to the damaged colon. DC subsequently relapsed in the entire colon and was refractory to the previous protocol and autologous faecal transplantation. Intravenous methylprednisolone and oral 5-ASA were discontinued owing to possible adverse effects. Infliximab with intravenous prednisolone was introduced, and the protocol was so effective in suppressing the acute colitis that total colectomy was avoided. The stoma was subsequently closed, and the patient is currently symptom-free. Infliximab is used for ulcerative colitis but could also be effective against severe DC.

Proposing a molecular classification associated with hypercoagulation in ovarian clear cell carcinoma

BACKGROUND

Although ovarian clear cell carcinoma (CCC) is associated with high incidence of thromboembolism, the clinicopathological and biological significance of hypercoagulable status in CCC remains unclear.

MATERIALS AND METHODS

We retrospectively analyzed pretreatment D-dimer levels, thromboembolic status, and clinical outcome of 125 CCCs in the discovery set and 143 CCCs in two other independent validation sets. Next, we performed RNA sequencing of 93 CCCs and compared coagulation-related gene profiles with 2492 pan-cancer data. We investigated differences in molecular characteristics of CCC subclasses based on coagulation status.

RESULTS

In the discovery dataset, D-dimer elevation above the normal range was significantly associated with shorter progression-free and overall survival, irrespective to thromboembolic status. Multivariate analysis identified D-dimer elevation and clinical stage as an independent prognostic factors. We confirmed the prognostic significance of D-dimer elevation in the validation sets. Tissue factor and IL6, which are considered key elements of cancer-induced hypercoagulation, were highly expressed in CCC than in other cancers regardless of D-dimer level. Higher activity of various oncogenic pathways was observed in CCC with compared to without D-dimer elevation. Moreover, hierarchical cluster analysis divided 57 CCCs with D-dimer elevation into immunologically hot and cold tumor subtypes. Hot tumors were characterized by enrichment of T-cell inflamed phenotype, inflammation, the epithelial-mesenchymal transition, and high serum levels of CRP, and cold tumors by enrichment of cell cycle and MYC pathways.

CONCLUSIONS

CCC represents hypercoagulable disease and elevate D-dimer is a prognostic factor for decreased survival in CCC. D-dimer high CCC has distinct molecular characteristics into the inflammatory-driven pathway (hot tumor) and the immune-suppressive pathway (cold tumor). Treatment implication of our proposed molecular classification merits further investigation.

The New Era of Three-Dimensional Histoarchitecture of the Human Endometrium

The histology of the endometrium has traditionally been established by observation of two-dimensional (2D) pathological sections. However, because human endometrial glands exhibit coiling and branching morphology, it is extremely difficult to obtain an entire image of the glands by 2D observation. In recent years, the development of three-dimensional (3D) reconstruction of serial pathological sections by computer and whole-mount imaging technology using tissue clearing methods with high-resolution fluorescence microscopy has enabled us to observe the 3D histoarchitecture of tissues. As a result, 3D imaging has revealed that human endometrial glands form a plexus network in the basalis, similar to the rhizome of grass, whereas mouse uterine glands are single branched tubular glands. This review summarizes the relevant literature on the 3D structure of mouse and human endometrium and discusses the significance of the rhizome structure in the human endometrium and the expected role of understanding the 3D tissue structure in future applications to systems biology.

Population pharmacokinetics of favipiravir in patients with COVID-19

The antiretroviral drug favipiravir (FPV) inhibits RNA‐dependent RNA polymerase. It has been developed for the treatment of the novel coronavirus (severe acute respiratory syndrome coronavirus 2) infection disease, coronavirus disease 2019 (COVID‐19). However, its pharmacokinetics in patients with COVID‐19 is poorly understood. In this study, we measured FPV serum concentration by liquid chromatography–tandem mass spectrometry and conducted population pharmacokinetic analysis. A total of 39 patients were enrolled in the study: 33 were administered FPV 1600 mg twice daily (b.i.d.) on the first day followed by 600 mg b.i.d., and 6 were administered FPV 1800 mg b.i.d. on the first day followed by 800 mg or 600 mg b.i.d. The median age was 68 years (range, 27–89 years), 31 (79.5%) patients were men, median body surface area (BSA) was 1.72 m² (range, 1.11–2.2 m²), and 10 (25.6%) patients required invasive mechanical ventilation (IMV) at the start of FPV. A total of 204 serum concentrations were available for pharmacokinetic analysis. A one‐compartment model with first‐order elimination was used to describe the pharmacokinetics. The estimated mean clearance/bioavailability (CL/F) and distribution volume/bioavailability (V/F) were 5.11 L/h and 41.6 L, respectively. Covariate analysis revealed that CL/F was significantly related to dosage, IMV use, and BSA. A simulation study showed that the 1600 mg/600 mg b.i.d. regimen was insufficient for the treatment of COVID‐19 targeting the 50% effective concentration (9.7 µg/mL), especially in patients with larger BSA and/or IMV. A higher FPV dosage is required for COVID‐19, but dose‐dependent nonlinear pharmacokinetics may cause an unexpected significant pharmacokinetic change and drug toxicity. Further studies are warranted to explore the optimal FPV regimen.

Atypical presentation at acute gastritis: significant gastric wall thickening as a presentation of a primary Helicobacter pylori infection in children

Helicobacter pylori infection could cause chronic inflammation in the stomach and induce peptic ulcer disease or even malignant tumour. The initial infection of the organism happens in childhood but most of cases are latent. We had a case of 10-year-old girl who presented with acute epigastric pain and significant thickening of the stomach wall on CT. The finding seemed atypical for acute gastritis so oesophagogastroduodenoscopy and serology examination were added and the primary infection of H. pylori was confirmed with the exclusion of other possible diagnoses like eosinophilic gastritis and IgA vasculitis. Acute gastritis is one of the most common sickness in children, however, it would be worthwhile considering further investigation including H. pylori infection in a case of atypical presentation to prevent negative consequences derived from chronic H. pylori infection.

Ultrasmall Downconverting Nanoparticle for Enhanced Cerenkov Imaging

Cerenkov imaging provides an opportunity to expand the application of approved radiotracers and therapeutic agents by utilizing them for optical approaches, which opens new avenues for nuclear imaging. The dominating Cerenkov radiation is in the UV/blue region, where it is readily absorbed by human tissue, reducing its utility in vivo. To solve this problem, we propose a strategy to shift Cerenkov light to the more penetrative red-light region through the use of a fluorescent down-conversion technique, based upon europium oxide nanoparticles. We synthesized square-shape ultrasmall Eu₂O₃ nanoparticles, functionalized with polyethylene glycol and chelate-free radiolabeled for intravenous injection into mice to visualize the lymph node and tumor. By adding trimethylamine N-oxide during the synthesis, we significantly increased the brightness of the particle and synthesized the (to-date) smallest radiolabeled europium-based nanoparticle. These features allow for the exploration of Eu₂O₃ nanoparticles as a preclinical cancer diagnosis platform with multimodal imaging capability.

Three-dimensional understanding of the morphological complexity of the human uterine endometrium

The fundamental morphology of the endometrial glands is not sufficiently understood by 2D observation because these glands have complicated winding and branching patterns. To construct a large picture of the endometrial gland structure, we performed tissue-clearing-based 3D imaging of human uterine endometrial tissue. Our 3D immunohistochemistry and layer analyses revealed that the endometrial glands form a plexus network in the stratum basalis and expand horizontally along the muscular layer, similar to the rhizome of grass. We then extended our method to assess the 3D morphology of tissue affected by adenomyosis, a representative "endometrium-related disease," and observed its 3D morphological features, including the direct invasion of endometrial glands into the myometrium and an ant colony-like network of ectopic endometrial glands within the myometrium. Thus, further understanding of the morphology of the human endometrium based on 3D analysis will lead to the identification of the pathogenesis of endometrium-related diseases.

Endoscopic Treatment of Sinonasal Leiomyosarcoma: A Case Report in Light of the Literature

A 49-year-old Japanese man presented with a rare case of sinonasal leiomyosarcoma with left nasal bleeding for 12 months. He had no history of irradiation or malignancies, including retinoblastoma. Preoperative histological examination suggested vascular leiomyoma. Complete resection with endoscopic surgery was performed. Histological examination during the operation suggested that the tumor was a leiomyoma. However, immunohistochemical staining for α smooth muscle actin and desmin were helpful in establishing a definitive diagnosis of sinonasal leiomyosarcoma. The resection margins were positive for tumor cells. Staging with CT of the neck and thorax, ultrasound of the abdomen, and MRI of the head ruled out metastases. Second endoscopic tumor resection surgery was performed for positive resection margins. The patient's condition was successfully managed with additional excision, and he remains well with no evidence of recurrence and metastasis 36 months after treatment. Endoscopic management should be considered in suitable cases.